This solution adds cell boundary (a filled mask) to an existing CellSketch project.
Tags
bdvcellsketch
Citation
https://doi.org/10.1083/jcb.202010039A. Müller, D. Schmidt, C. S. Xu, S. Pang, J. V. D'Costa, S. Kretschmar, C. Münster, T. Kurth, F. Jug, M. Weigert, H. F. Hess, M. Solimena; 3D FIB-SEM reconstruction of microtubule-organelle interaction in whole primary mouse β cells. J Cell Biol 1 February 2021; 220 (2): e202010039.
Solution written by
Deborah Schmidt
Arguments
--project
The CellSketch project to be opened (.n5). (default value: PARAMETER_VALUE)
--input
The dataset file (3D, filled mask) (default value: PARAMETER_VALUE)
--name
The name of the dataset (default value: PARAMETER_VALUE)
--scale_x
Scale factor X for input dataset (default value: 1)
--scale_y
Scale factor Y of input dataset (default value: 1)
--scale_z
Scale factor Z of input dataset (default value: 1)
--color
Color of dataset in RGBA separated by ":" (i.e. 255:255:0:255) (default value: 255:155:0:255)
--analyzeConnectionFilamentEnds
Analyze connection to filaments ends (default value: 0)
--thresholdConnectionFilamentEnds
Threshold to count filament ends as connected in um (default value: PARAMETER_VALUE)
Usage instructions
Please follow this link for details on how to install and run this solution.
